Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```If links are relative path to local files, they should be relative to the markdown file.
Images are lazy-loaded.
<!-- no empty lines among the images -->



Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```If links are relative path to local files, they should be relative to the markdown file.
Images are lazy-loaded.
<!-- no empty lines among the images -->



Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```If links are relative path to local files, they should be relative to the markdown file.
Images are lazy-loaded.
<!-- no empty lines among the images -->



Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::[[Pypi][[2]](#PYPPL-REF-2){.pyppl-report-refindex}][[3]](#PYPPL-REF-3){.pyppl-report-refindex} [[Github][[4]](#PYPPL-REF-4){.pyppl-report-refindex}][[5]](#PYPPL-REF-5){.pyppl-report-refindex} [[PyPPL][[6]](#PYPPL-REF-6){.pyppl-report-refindex}][[7]](#PYPPL-REF-7){.pyppl-report-refindex} [[PythonVers][[8]](#PYPPL-REF-8){.pyppl-report-refindex}][[3]](#PYPPL-REF-3){.pyppl-report-refindex} [[docs][[9]](#PYPPL-REF-9){.pyppl-report-refindex}][[10]](#PYPPL-REF-10){.pyppl-report-refindex} [[Travis building][[11]](#PYPPL-REF-11){.pyppl-report-refindex}][[12]](#PYPPL-REF-12){.pyppl-report-refindex} [[Codacy][[13]](#PYPPL-REF-13){.pyppl-report-refindex}][[14]](#PYPPL-REF-14){.pyppl-report-refindex} [[Codacy coverage][[15]](#PYPPL-REF-15){.pyppl-report-refindex}][[14]](#PYPPL-REF-14){.pyppl-report-refindex}
A report generating system for [PyPPL][[7]](#PYPPL-REF-7){.pyppl-report-refindex}
Requires pandoc 2.7+ (and wkhtmltopdf 0.12.4+ when creating PDF reports)
pyppl_report requires pandoc/wkhtmltopdf to be installed in $PATH
pip install pyppl_report
pPyClone.config.report_template = """
# {{report.title}}
PyClone[[7]](#PYPPL-REF-7){.pyppl-report-refindex} is a tool using Probabilistic model for inferring clonal population
structure from deep NGS sequencing.
}})
```table
caption: Clusters
file: "{{path.join(job.o.outdir, "tables/cluster.tsv")}}"
rows: 10
```
Nature methods 11.4 (2014): 396.
"""
# or use a template file
pPyClone.config.report_template = "file:/path/to/template.md"PyPPL().start(pPyClone).run().report(
'/path/to/report',
title='Clonality analysis using PyClone',
template='bootstrap'
)
# or save report in a directory
PyPPL(name='Awesome-pipeline').start(pPyClone).run().report('/path/to/')
# report generated at ./Awesome-pipeline.report.htmlYou can generate a toml file named job.report.data.toml under <job.outdir> with extra data to render the report template. Beyond that, proc attributes and args can also be used.
For example: job.report.data.toml:
description = 'A awesome report for job 1'
Then in your template, you can use it:
We use [[7]](#PYPPL-REF-7){.pyppl-report-refindex}, [[10]](#PYPPL-REF-10){.pyppl-report-refindex} … to link to the references, so HTML links have to be in-place (in the format of [text](link) instead of [text][link-index]). All references from different processes will be re-ordered and combined.
[1]: ref1[2]: https://img.shields.io/pypi/v/pyppl_report?style=flat-square[3]: https://pypi.org/project/pyppl_report/[4]: https://img.shields.io/github/tag/pwwang/pyppl_report?style=flat-square[5]: https://github.com/pwwang/pyppl_report[6]: https://img.shields.io/github/tag/pwwang/pyppl?label=PyPPL&style=flat-square[7]: https://github.com/pwwang/PyPPL[8]: https://img.shields.io/pypi/pyversions/pyppl_report?style=flat-square[9]: https://img.shields.io/readthedocs/pyppl_report.svg?style=flat-square[10]: https://pyppl_report.readthedocs.io/en/latest/[11]: https://img.shields.io/travis/pwwang/pyppl_report?style=flat-square[12]: https://travis-ci.org/pwwang/pyppl_report[13]: https://img.shields.io/codacy/grade/2b7914a18f794248a62d7b36eb2408a3?style=flat-square[14]: https://app.codacy.com/manual/pwwang/pyppl_report/dashboard[15]: https://img.shields.io/codacy/coverage/2b7914a18f794248a62d7b36eb2408a3?style=flat-square